Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli

Abstract While most restriction enzymes catalyze the hydrolysis of phosphodiester bonds at specific nucleotide sequences in DNA, restriction enzymes of the HALFPIPE superfamily cleave N-glycosidic bonds, similar to DNA glycosylases. Apurinic/apyrimidinic (AP) sites generated by HALFPIPE superfamily...

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Autores principales:	Ken-ichi Miyazono, Delong Wang, Tomoko Ito, Masaru Tanokura
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fb68d9af990646118b516f63dd5714ec
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spelling	oai:doaj.org-article:fb68d9af990646118b516f63dd5714ec2021-12-02T14:01:32ZCrystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli10.1038/s41598-020-79537-y2045-2322https://doaj.org/article/fb68d9af990646118b516f63dd5714ec2021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-79537-yhttps://doaj.org/toc/2045-2322Abstract While most restriction enzymes catalyze the hydrolysis of phosphodiester bonds at specific nucleotide sequences in DNA, restriction enzymes of the HALFPIPE superfamily cleave N-glycosidic bonds, similar to DNA glycosylases. Apurinic/apyrimidinic (AP) sites generated by HALFPIPE superfamily proteins are cleaved by their inherent AP lyase activities, other AP endonuclease activities or heat-promoted β-elimination. Although the HALFPIPE superfamily protein R.PabI, obtained from a hyperthermophilic archaea, Pyrococcus abyssi, shows weak AP lyase activity, HALFPIPE superfamily proteins in mesophiles, such as R.CcoLI from Campylobacter coli and R. HpyAXII from Helicobacter pylori, show significant AP lyase activities. To identify the structural basis for the AP lyase activity of R.CcoLI, we determined the structure of R.CcoLI by X-ray crystallography. The structure of R.CcoLI, obtained at 2.35-Å resolution, shows that a conserved lysine residue (Lys71), which is stabilized by a characteristic β-sheet structure of R.CcoLI, protrudes into the active site. The results of mutational assays indicate that Lys71 is important for the AP lyase activity of R.CcoLI. Our results help to elucidate the mechanism by which HALFPIPE superfamily proteins from mesophiles efficiently introduce double-strand breaks to specific sites on double-stranded DNA.Ken-ichi MiyazonoDelong WangTomoko ItoMasaru TanokuraNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ken-ichi Miyazono Delong Wang Tomoko Ito Masaru Tanokura Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli
description	Abstract While most restriction enzymes catalyze the hydrolysis of phosphodiester bonds at specific nucleotide sequences in DNA, restriction enzymes of the HALFPIPE superfamily cleave N-glycosidic bonds, similar to DNA glycosylases. Apurinic/apyrimidinic (AP) sites generated by HALFPIPE superfamily proteins are cleaved by their inherent AP lyase activities, other AP endonuclease activities or heat-promoted β-elimination. Although the HALFPIPE superfamily protein R.PabI, obtained from a hyperthermophilic archaea, Pyrococcus abyssi, shows weak AP lyase activity, HALFPIPE superfamily proteins in mesophiles, such as R.CcoLI from Campylobacter coli and R. HpyAXII from Helicobacter pylori, show significant AP lyase activities. To identify the structural basis for the AP lyase activity of R.CcoLI, we determined the structure of R.CcoLI by X-ray crystallography. The structure of R.CcoLI, obtained at 2.35-Å resolution, shows that a conserved lysine residue (Lys71), which is stabilized by a characteristic β-sheet structure of R.CcoLI, protrudes into the active site. The results of mutational assays indicate that Lys71 is important for the AP lyase activity of R.CcoLI. Our results help to elucidate the mechanism by which HALFPIPE superfamily proteins from mesophiles efficiently introduce double-strand breaks to specific sites on double-stranded DNA.
format	article
author	Ken-ichi Miyazono Delong Wang Tomoko Ito Masaru Tanokura
author_facet	Ken-ichi Miyazono Delong Wang Tomoko Ito Masaru Tanokura
author_sort	Ken-ichi Miyazono
title	Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli
title_short	Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli
title_full	Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli
title_fullStr	Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli
title_full_unstemmed	Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli
title_sort	crystal structure and dna cleavage mechanism of the restriction dna glycosylase r.ccoli from campylobacter coli
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/fb68d9af990646118b516f63dd5714ec
work_keys_str_mv	AT kenichimiyazono crystalstructureanddnacleavagemechanismoftherestrictiondnaglycosylaserccolifromcampylobactercoli AT delongwang crystalstructureanddnacleavagemechanismoftherestrictiondnaglycosylaserccolifromcampylobactercoli AT tomokoito crystalstructureanddnacleavagemechanismoftherestrictiondnaglycosylaserccolifromcampylobactercoli AT masarutanokura crystalstructureanddnacleavagemechanismoftherestrictiondnaglycosylaserccolifromcampylobactercoli
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Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli

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